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ModelSEED / PlantSEED

Repository for containing code and files that pertain to the use of PlantSEED in the ModelSEED environment
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How can I used PlantSEED for annotate plant transcripts with metabolic functions ? #19

Open anani-a-missinou opened 4 years ago

anani-a-missinou commented 4 years ago

Hi dear Seaver?

I’m a Ph.D. student in France on Brassica napus (rapeseed) specialized metabolites against pathogens.

I want to apply your tool on my Brassica napus transcriptome to annotate transcripts with metabolic functions. Compare to A. thaliana , this species has 6 copy of genes from genes polyploidization and more than 6 copies for certain genes which have undergone tandem duplication and which have not been purified during evolution.

Does your tool manage the fate of these genes (neofunctionalization vs subfunctionalization of multiple gene copies)?

Best regards A. A. Missinou

samseaver commented 4 years ago

Dear A. A. Missinou,

Sorry for the delay in replying.

As I want to understand, you're talking about using our tool for building a plant metabolic reconstruction at https://modelseed.org? The underlying algorithm uses k-mers, as described in our paper. While it does have some success, the process by which k-mers are generated, and then applied, ignores gene duplication events entirely. If the duplication event happened relatively recently, then we'd confidently expect the multiple gene copies to be "hit" by the same k-mers, but beyond that, the tool doesn't address any sequence divergence.

On the other hand, we do use plant protein families and sequence alignments (as generated by OrthoFinder) in our more recent App developed for use in a KBase (https://kbase.us) narrative (https://narrative.kbase.us). While the tool does not present the gene trees that result from the use of OrthoFinder, I would be happy to work with you to get you the data you need to help understand how the functionalization of different enzymes may be diverging. Please do follow up with me directly at samseaver@gmail.com

Finally, I note that you mention specialized metabolites, the PlantSEED project was primarily focused on primary metabolism, though we've curated a few intermediate metabolic pathways key for several cofactors, and thereby contain several precursors for secondary metabolites.

Thanks Sam